[English] 日本語
Yorodumi
- EMDB-31969: Cryo-EM structure of the human P4-type flippase ATP8B1-CDC50B in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31969
TitleCryo-EM structure of the human P4-type flippase ATP8B1-CDC50B in the auto-inhibited E2P state
Map data
Sample
  • Complex: ATP8B1-CDC50B complex
    • Protein or peptide: Cell cycle control protein 50B
    • Protein or peptide: Phospholipid-transporting ATPase IC
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


vestibulocochlear nerve formation / regulation of plasma membrane organization / regulation of microvillus assembly / phosphatidylcholine flippase activity / aminophospholipid flippase activity / aminophospholipid transport / phosphatidylserine flippase activity / inner ear receptor cell development / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity ...vestibulocochlear nerve formation / regulation of plasma membrane organization / regulation of microvillus assembly / phosphatidylcholine flippase activity / aminophospholipid flippase activity / aminophospholipid transport / phosphatidylserine flippase activity / inner ear receptor cell development / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity / phosphatidylserine floppase activity / positive regulation of protein exit from endoplasmic reticulum / cardiolipin binding / xenobiotic transmembrane transport / apical protein localization / phosphatidylcholine floppase activity / stereocilium / bile acid metabolic process / P-type phospholipid transporter / bile acid and bile salt transport / phospholipid translocation / Golgi organization / Ion transport by P-type ATPases / monoatomic ion transmembrane transport / regulation of chloride transport / sensory perception of sound / trans-Golgi network / membrane => GO:0016020 / nuclear body / apical plasma membrane / negative regulation of DNA-templated transcription / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / ATP hydrolysis activity / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Cell cycle control protein 50B / CDC50/LEM3 family / LEM3 (ligand-effect modulator 3) family / CDC50 family / P-type ATPase, subfamily IV / P-type ATPase, C-terminal / P-type ATPase, N-terminal / Phospholipid-translocating ATPase N-terminal / Phospholipid-translocating P-type ATPase C-terminal / Cation transport ATPase (P-type) / E1-E2 ATPase ...Cell cycle control protein 50B / CDC50/LEM3 family / LEM3 (ligand-effect modulator 3) family / CDC50 family / P-type ATPase, subfamily IV / P-type ATPase, C-terminal / P-type ATPase, N-terminal / Phospholipid-translocating ATPase N-terminal / Phospholipid-translocating P-type ATPase C-terminal / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Phospholipid-transporting ATPase IC / Cell cycle control protein 50B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsChen MT / Chen Y
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508500 China
Chinese Academy of SciencesXDB37020202 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural insights into the activation of autoinhibited human lipid flippase ATP8B1 upon substrate binding.
Authors: Meng-Ting Cheng / Yu Chen / Zhi-Peng Chen / Xin Liu / Zhiyong Zhang / Yuxing Chen / Wen-Tao Hou / Cong-Zhao Zhou /
Abstract: SignificanceATP8B1 is a P4 ATPase that maintains membrane asymmetry by transporting phospholipids across the cell membrane. Disturbance of lipid asymmetry will lead to the imbalance of the cell ...SignificanceATP8B1 is a P4 ATPase that maintains membrane asymmetry by transporting phospholipids across the cell membrane. Disturbance of lipid asymmetry will lead to the imbalance of the cell membrane and eventually, cell death. Thus, defects in ATP8B1 are usually associated with severe human diseases, such as intrahepatic cholestasis. The present structures of ATP8B1 complexed with its auxiliary noncatalytic partners CDC50A and CDC50B reveal an autoinhibited state of ATP8B1 that could be released upon substrate binding. Moreover, release of this autoinhibition could be facilitated by the bile acids, which are key factors that alter the membrane asymmetry of hepatocytes. This enabled us to figure out a feedback loop of bile acids and lipids across the cell membrane.
History
DepositionSep 16, 2021-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateOct 12, 2022-
Current statusOct 12, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_31969.png

Downloads & links

-
Map

FileDownload / File: emd_31969.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.074 Å
Density
Contour LevelBy AUTHOR: 0.0125
Minimum - Maximum-0.05258281 - 0.10495735
Average (Standard dev.)0.00010610517 (±0.0039366055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 257.76 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : ATP8B1-CDC50B complex

EntireName: ATP8B1-CDC50B complex
Components
  • Complex: ATP8B1-CDC50B complex
    • Protein or peptide: Cell cycle control protein 50B
    • Protein or peptide: Phospholipid-transporting ATPase IC
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: ATP8B1-CDC50B complex

SupramoleculeName: ATP8B1-CDC50B complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

-
Macromolecule #1: Cell cycle control protein 50B

MacromoleculeName: Cell cycle control protein 50B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.307391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSHHHHHHGS GSMTWSATAR GAHQPDNTAF TQQRLPAWQP LLSASIALPL FFCAGLAFIG LGLGLYYSSN GIKELEYDYT GDPGTGNCS VCAAAGQGRA LPPPCSCAWY FSLPELFQGP VYLYYELTNF YQNNRRYGVS RDDAQLSGLP SALRHPVNEC A PYQRSAAG ...String:
MSHHHHHHGS GSMTWSATAR GAHQPDNTAF TQQRLPAWQP LLSASIALPL FFCAGLAFIG LGLGLYYSSN GIKELEYDYT GDPGTGNCS VCAAAGQGRA LPPPCSCAWY FSLPELFQGP VYLYYELTNF YQNNRRYGVS RDDAQLSGLP SALRHPVNEC A PYQRSAAG LPIAPCGAIA NSLFNDSFSL WHQRQPGGPY VEVPLDRSGI AWWTDYHVKF RNPPLVNGSL ALAFQGTAPP PN WRRPVYE LSPDPNNTGF INQDFVVWMR TAALPTFRKL YARIRQGNYS AGLPRGAYRV NITYNYPVRA FGGHKLLIFS SIS WMGGKN PFLGIAYLVV GSLCILTGFV MLVVYIRYQD QDDDDEE

-
Macromolecule #2: Phospholipid-transporting ATPase IC

MacromoleculeName: Phospholipid-transporting ATPase IC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type phospholipid transporter
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 148.538547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMSTERDS ETTFDEDSQP NDEVVPYSDD ETEDELDDQG SAVEPEQNR VNREAEENRE PFRKECTWQV KANDRKYHEQ PHFMNTKFLC IKESKYANNA IKTYKYNAFT FIPMNLFEQF K RAANLYFL ...String:
MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMSTERDS ETTFDEDSQP NDEVVPYSDD ETEDELDDQG SAVEPEQNR VNREAEENRE PFRKECTWQV KANDRKYHEQ PHFMNTKFLC IKESKYANNA IKTYKYNAFT FIPMNLFEQF K RAANLYFL ALLILQAVPQ ISTLAWYTTL VPLLVVLGVT AIKDLVDDVA RHKMDKEINN RTCEVIKDGR FKVAKWKEIQ VG DVIRLKK NDFVPADILL LSSSEPNSLC YVETAELDGE TNLKFKMSLE ITDQYLQRED TLATFDGFIE CEEPNNRLDK FTG TLFWRN TSFPLDADKI LLRGCVIRNT DFCHGLVIFA GADTKIMKNS GKTRFKRTKI DYLMNYMVYT IFVVLILLSA GLAI GHAYW EAQVGNSSWY LYDGEDDTPS YRGFLIFWGY IIVLNTMVPI SLYVSVEVIR LGQSHFINWD LQMYYAEKDT PAKAR TTTL NEQLGQIHYI FS(PHD)KTGTLTQ NIMTFKKCCI NGQIYGDHRD ASQHNHNKIE QVDFSWNTYA DGKLAFYDHY LI EQIQSGK EPEVRQFFFL LAVCHTVMVD RTDGQLNYQA ASPDEGALVN AARNFGFAFL ARTQNTITIS ELGTERTYNV LAI LDFNSD RKRMSIIVRT PEGNIKLYCK GADTVIYERL HRMNPTKQET QDALDIFANE TLRTLCLCYK EIEEKEFTEW NKKF MAASV ASTNRDEALD KVYEEIEKDL ILLGATAIED KLQDGVPETI SKLAKADIKI WVLTGDKKET AENIGFACEL LTEDT TICY GEDINSLLHA RMENQRNRGG VYAKFAPPVQ ESFFPPGGNR ALIITGSWLN EILLEKKTKR NKILKLKFPR TEEERR MRT QSKRRLEAKK EQRQKNFVDL ACECSAVICC RVTPKQKAMV VDLVKRYKKA ITLAIGDGAN DVNMIKTAHI GVGISGQ EG MQAVMSSDYS FAQFRYLQRL LLVHGRWSYI RMCKFLRYFF YKNFAFTLVH FWYSFFNGYS AQTAYEDWFI TLYNVLYT S LPVLLMGLLD QDVSDKLSLR FPGLYIVGQR DLLFNYKRFF VSLLHGVLTS MILFFIPLGA YLQTVGQDGE APSDYQSFA VTIASALVIT VNFQIGLDTS YWTFVNAFSI FGSIALYFGI MFDFHSAGIH VLFPSAFQFT GTASNALRQP YIWLTIILAV AVCLLPVVA IRFLSMTIWP SESDKIQKHR KRLKAEEQWQ RRQQVFRRGV STRRSAYAFS HQRGYADLIS SGRSIRKKRS P LDAIVADG TAEYRRTGDS

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160435
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more